Zinc in PDB 8vkt: Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium

All present enzymatic activity of Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium:
3.5.1.18;

The structure of Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium, PDB code: 8vkt was solved by L.Gonzalez-Segura, A.Diaz-Vilchis, M.Terrazas-Lopez, A.G.Diaz-Sanchez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.37 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.822, 44.914, 78.024, 90, 104.28, 90
R / Rfree (%)	15.4 / 17.6

The binding sites of Zinc atom in the Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium (pdb code 8vkt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium, PDB code: 8vkt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.2 occ:0.83 O A:HOH746 1.9 18.6 1.0 OE1 A:GLU164 1.9 14.8 1.0 OD1 A:ASP104 2.0 15.3 1.0 NE2 A:HIS71 2.0 12.7 1.0 CD A:GLU164 2.7 16.4 1.0 OE2 A:GLU164 2.7 16.8 1.0 CG A:ASP104 3.0 17.0 1.0 CE1 A:HIS71 3.0 13.7 1.0 CD2 A:HIS71 3.1 12.3 1.0 OD2 A:ASP104 3.3 24.1 1.0 ZN A:ZN402 3.4 17.3 0.2 OE2 A:GLU139 3.7 22.1 1.0 OE1 A:GLU138 3.7 17.1 1.0 O A:HOH850 3.8 44.6 1.0 O A:HOH754 3.9 32.6 1.0 CG A:MET105 4.1 12.7 1.0 ND1 A:HIS71 4.1 13.6 1.0 CG A:GLU164 4.1 15.4 1.0 CG A:HIS71 4.2 12.5 1.0 CB A:MET105 4.2 12.6 1.0 CB A:ASP104 4.3 15.9 1.0 CD A:GLU138 4.4 18.9 1.0 SD A:MET105 4.4 13.1 1.0 CD A:GLU139 4.5 20.2 1.0 C A:ASP104 4.6 14.5 1.0 CA A:ASP104 4.6 14.2 1.0 CB A:GLU164 4.8 13.4 1.0 N A:MET105 4.8 12.1 1.0 CD A:PRO165 4.8 13.4 1.0 OE2 A:GLU138 4.8 22.7 1.0 O A:ASP104 4.9 14.9 1.0 OE1 A:GLU139 4.9 21.2 1.0 O A:HOH948 4.9 36.2 1.0

Zinc binding site 2 out of 2 in the Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Structure of Dimetalated Dape From Enterococcus Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.3 occ:0.25 OE2 A:GLU139 2.1 22.1 1.0 O A:HOH746 2.1 18.6 1.0 OD2 A:ASP104 2.1 24.1 1.0 NE2 A:HIS352 2.3 24.0 1.0 OE1 A:GLU139 2.5 21.2 1.0 CD A:GLU139 2.6 20.2 1.0 CE1 A:HIS352 3.1 27.5 1.0 CG A:ASP104 3.1 17.0 1.0 O A:HOH850 3.3 44.6 1.0 CD2 A:HIS352 3.3 24.9 1.0 ZN A:ZN401 3.4 14.2 0.8 OD1 A:ASP104 3.4 15.3 1.0 CG A:GLU139 4.0 17.6 1.0 OE1 A:GLU138 4.2 17.1 1.0 O A:HOH675 4.2 17.3 1.0 O A:HOH754 4.3 32.6 1.0 O A:HOH704 4.3 31.4 1.0 ND1 A:HIS352 4.3 28.3 1.0 CB A:ASP104 4.4 15.9 1.0 CG A:HIS352 4.4 21.9 1.0 NE2 A:HIS71 4.5 12.7 1.0 CE1 A:HIS71 4.7 13.7 1.0 CG1 A:VAL75 4.8 18.0 1.0 OE1 A:GLU164 4.8 14.8 1.0 O A:HOH657 4.8 37.5 1.0

M.Terrazas-Lopez, L.Gonzalez-Segura, A.Diaz-Vilchis, K.A.Aguirre-Mendez, N.Lobo-Galo, A.Martinez-Martinez, A.G.Diaz-Sanchez. The Three-Dimensional Structure of Dape From Enterococcus Faecium Reveals New Insights Into Dape/Arge Subfamily Ligand Specificity. Int.J.Biol.Macromol. 32281 2024.
ISSN: ISSN 0141-8130
PubMed: 38740150
DOI: 10.1016/J.IJBIOMAC.2024.132281